Merge pull request #177 from sandialabs/efjc-isometric-legendre

EFJC isometric legendre

Cargo.toml

@@ -1,6 +1,6 @@
 [package]
 name = "polymers"
-version = "0.3.1"
+version = "0.3.2"
 edition = "2021"
 description = "Polymers Modeling Library"
 license = "BSD-3-Clause"

Dockerfile

@@ -9,4 +9,4 @@ RUN pip install --no-cache-dir maturin && \
     pip install --no-cache-dir target/wheels/*.whl
 COPY --from=julia /usr/local/julia/ /opt/julia/
 ENV PATH "${PATH}:/opt/julia/bin"
-RUN julia -e 'using Pkg; Pkg.develop(path="."); Pkg.build("Polymers"); Pkg.test("Polymers")'
+RUN julia -e 'using Pkg; Pkg.develop(path="."); Pkg.build("Polymers")'

Project.toml

@@ -1,7 +1,7 @@
 name = "Polymers"
 uuid = "8aef037c-a721-4e8a-9d81-eb7093daef2c"
 authors = ["mrbuche <mrbuche@sandia.gov>"]
-version = "0.3.1"
+version = "0.3.2"
 
 [deps]
 DocStringExtensions = "ffbed154-4ef7-542d-bbb7-c09d3a79fcae"

docs/source/physics/single_chain/efjc/thermodynamics.rst

@@ -4,6 +4,7 @@ EFJC model thermodynamics
 .. toctree::
    :maxdepth: 1
 
+   Isometric <thermodynamics/isometric>
    Isotensional <thermodynamics/isotensional>
 
 .. autoclass:: polymers.physics.single_chain.efjc.thermodynamics::EFJC(number_of_links, link_length, hinge_mass, link_stiffness)
@@ -12,4 +13,5 @@ EFJC model thermodynamics
    .. autoattribute:: link_length
    .. autoattribute:: hinge_mass
    .. autoattribute:: link_stiffness
+   .. autoattribute:: isometric
    .. autoattribute:: isotensional

docs/source/physics/single_chain/efjc/thermodynamics/isometric.rst

@@ -0,0 +1,17 @@
+EFJC model thermodynamics (isometric)
+=====================================
+
+.. toctree::
+   :maxdepth: 1
+
+   Asymptotic <isometric/asymptotic>
+   Legendre <isometric/legendre>
+
+.. autoclass:: polymers.physics.single_chain.efjc.thermodynamics.isometric::EFJC(number_of_links, link_length, hinge_mass, link_stiffness)
+
+   .. autoattribute:: number_of_links
+   .. autoattribute:: link_length
+   .. autoattribute:: hinge_mass
+   .. autoattribute:: link_stiffness
+   .. autoattribute:: asymptotic
+   .. autoattribute:: legendre

docs/source/physics/single_chain/efjc/thermodynamics/isometric/asymptotic.rst

@@ -0,0 +1,19 @@
+EFJC model thermodynamics (isometric/asymptotic)
+================================================
+
+.. toctree::
+   :maxdepth: 1
+
+   Alternative <asymptotic/alternative>
+   Reduced <asymptotic/reduced>
+   Legendre <asymptotic/legendre>
+
+.. autoclass:: polymers.physics.single_chain.efjc.thermodynamics.isometric.asymptotic::EFJC(number_of_links, link_length, hinge_mass, link_stiffness)
+
+   .. autoattribute:: number_of_links
+   .. autoattribute:: link_length
+   .. autoattribute:: hinge_mass
+   .. autoattribute:: link_stiffness
+   .. autoattribute:: alternative
+   .. autoattribute:: reduced
+   .. autoattribute:: legendre

docs/source/physics/single_chain/efjc/thermodynamics/isometric/asymptotic/alternative.rst

@@ -0,0 +1,15 @@
+EFJC model thermodynamics (isometric/asymptotic/alternative)
+============================================================
+
+.. toctree::
+   :maxdepth: 1
+
+   Legendre <alternative/legendre>
+
+.. autoclass:: polymers.physics.single_chain.efjc.thermodynamics.isometric.asymptotic.alternative::EFJC(number_of_links, link_length, hinge_mass, link_stiffness)
+
+   .. autoattribute:: number_of_links
+   .. autoattribute:: link_length
+   .. autoattribute:: hinge_mass
+   .. autoattribute:: link_stiffness
+   .. autoattribute:: legendre

docs/source/physics/single_chain/efjc/thermodynamics/isometric/asymptotic/alternative/legendre.rst

@@ -0,0 +1,19 @@
+EFJC model thermodynamics (isometric/asymptotic/alternative/legendre)
+=====================================================================
+
+.. autoclass:: polymers.physics.single_chain.efjc.thermodynamics.isometric.asymptotic.alternative.legendre::EFJC(number_of_links, link_length, hinge_mass, link_stiffness)
+
+   .. autoattribute:: number_of_links
+   .. autoattribute:: link_length
+   .. autoattribute:: hinge_mass
+   .. autoattribute:: link_stiffness
+   .. automethod:: force(end_to_end_length, temperature)
+   .. automethod:: nondimensional_force(nondimensional_end_to_end_length_per_link)
+   .. automethod:: helmholtz_free_energy(end_to_end_length, temperature)
+   .. automethod:: helmholtz_free_energy_per_link(end_to_end_length, temperature)
+   .. automethod:: relative_helmholtz_free_energy(end_to_end_length, temperature)
+   .. automethod:: relative_helmholtz_free_energy_per_link(end_to_end_length, temperature)
+   .. automethod:: nondimensional_helmholtz_free_energy(nondimensional_end_to_end_length_per_link, temperature)
+   .. automethod:: nondimensional_helmholtz_free_energy_per_link(nondimensional_end_to_end_length_per_link, temperature)
+   .. automethod:: nondimensional_relative_helmholtz_free_energy(nondimensional_end_to_end_length_per_link)
+   .. automethod:: nondimensional_relative_helmholtz_free_energy_per_link(nondimensional_end_to_end_length_per_link)

docs/source/physics/single_chain/efjc/thermodynamics/isometric/asymptotic/legendre.rst

@@ -0,0 +1,19 @@
+EFJC model thermodynamics (isometric/asymptotic/legendre)
+=========================================================
+
+.. autoclass:: polymers.physics.single_chain.efjc.thermodynamics.isometric.asymptotic.legendre::EFJC(number_of_links, link_length, hinge_mass, link_stiffness)
+
+   .. autoattribute:: number_of_links
+   .. autoattribute:: link_length
+   .. autoattribute:: hinge_mass
+   .. autoattribute:: link_stiffness
+   .. automethod:: force(end_to_end_length, temperature)
+   .. automethod:: nondimensional_force(nondimensional_end_to_end_length_per_link)
+   .. automethod:: helmholtz_free_energy(end_to_end_length, temperature)
+   .. automethod:: helmholtz_free_energy_per_link(end_to_end_length, temperature)
+   .. automethod:: relative_helmholtz_free_energy(end_to_end_length, temperature)
+   .. automethod:: relative_helmholtz_free_energy_per_link(end_to_end_length, temperature)
+   .. automethod:: nondimensional_helmholtz_free_energy(nondimensional_end_to_end_length_per_link, temperature)
+   .. automethod:: nondimensional_helmholtz_free_energy_per_link(nondimensional_end_to_end_length_per_link, temperature)
+   .. automethod:: nondimensional_relative_helmholtz_free_energy(nondimensional_end_to_end_length_per_link)
+   .. automethod:: nondimensional_relative_helmholtz_free_energy_per_link(nondimensional_end_to_end_length_per_link)

docs/source/physics/single_chain/efjc/thermodynamics/isometric/asymptotic/reduced.rst

@@ -0,0 +1,15 @@
+EFJC model thermodynamics (isometric/asymptotic/reduced)
+========================================================
+
+.. toctree::
+   :maxdepth: 1
+
+   Legendre <reduced/legendre>
+
+.. autoclass:: polymers.physics.single_chain.efjc.thermodynamics.isometric.asymptotic.reduced::EFJC(number_of_links, link_length, hinge_mass, link_stiffness)
+
+   .. autoattribute:: number_of_links
+   .. autoattribute:: link_length
+   .. autoattribute:: hinge_mass
+   .. autoattribute:: link_stiffness
+   .. autoattribute:: legendre

docs/source/physics/single_chain/efjc/thermodynamics/isometric/asymptotic/reduced/legendre.rst

@@ -0,0 +1,19 @@
+EFJC model thermodynamics (isometric/asymptotic/reduced/legendre)
+=================================================================
+
+.. autoclass:: polymers.physics.single_chain.efjc.thermodynamics.isometric.asymptotic.reduced.legendre::EFJC(number_of_links, link_length, hinge_mass, link_stiffness)
+
+   .. autoattribute:: number_of_links
+   .. autoattribute:: link_length
+   .. autoattribute:: hinge_mass
+   .. autoattribute:: link_stiffness
+   .. automethod:: force(end_to_end_length, temperature)
+   .. automethod:: nondimensional_force(nondimensional_end_to_end_length_per_link)
+   .. automethod:: helmholtz_free_energy(end_to_end_length, temperature)
+   .. automethod:: helmholtz_free_energy_per_link(end_to_end_length, temperature)
+   .. automethod:: relative_helmholtz_free_energy(end_to_end_length, temperature)
+   .. automethod:: relative_helmholtz_free_energy_per_link(end_to_end_length, temperature)
+   .. automethod:: nondimensional_helmholtz_free_energy(nondimensional_end_to_end_length_per_link, temperature)
+   .. automethod:: nondimensional_helmholtz_free_energy_per_link(nondimensional_end_to_end_length_per_link, temperature)
+   .. automethod:: nondimensional_relative_helmholtz_free_energy(nondimensional_end_to_end_length_per_link)
+   .. automethod:: nondimensional_relative_helmholtz_free_energy_per_link(nondimensional_end_to_end_length_per_link)

docs/source/physics/single_chain/efjc/thermodynamics/isometric/legendre.rst

@@ -0,0 +1,19 @@
+EFJC model thermodynamics (isometric/legendre)
+==============================================
+
+.. autoclass:: polymers.physics.single_chain.efjc.thermodynamics.isometric.legendre::EFJC(number_of_links, link_length, hinge_mass, link_stiffness)
+
+   .. autoattribute:: number_of_links
+   .. autoattribute:: link_length
+   .. autoattribute:: hinge_mass
+   .. autoattribute:: link_stiffness
+   .. automethod:: force(end_to_end_length, temperature)
+   .. automethod:: nondimensional_force(nondimensional_end_to_end_length_per_link)
+   .. automethod:: helmholtz_free_energy(end_to_end_length, temperature)
+   .. automethod:: helmholtz_free_energy_per_link(end_to_end_length, temperature)
+   .. automethod:: relative_helmholtz_free_energy(end_to_end_length, temperature)
+   .. automethod:: relative_helmholtz_free_energy_per_link(end_to_end_length, temperature)
+   .. automethod:: nondimensional_helmholtz_free_energy(nondimensional_end_to_end_length_per_link, temperature)
+   .. automethod:: nondimensional_helmholtz_free_energy_per_link(nondimensional_end_to_end_length_per_link, temperature)
+   .. automethod:: nondimensional_relative_helmholtz_free_energy(nondimensional_end_to_end_length_per_link)
+   .. automethod:: nondimensional_relative_helmholtz_free_energy_per_link(nondimensional_end_to_end_length_per_link)

docs/source/physics/single_chain/swfjc/thermodynamics.rst

@@ -4,6 +4,7 @@ SWFJC model thermodynamics
 .. toctree::
    :maxdepth: 1
 
+   Isometric <thermodynamics/isometric>
    Isotensional <thermodynamics/isotensional>
 
 .. autoclass:: polymers.physics.single_chain.swfjc.thermodynamics::SWFJC(number_of_links, link_length, hinge_mass, well_width)
@@ -12,4 +13,5 @@ SWFJC model thermodynamics
    .. autoattribute:: link_length
    .. autoattribute:: hinge_mass
    .. autoattribute:: well_width
+   .. autoattribute:: isometric
    .. autoattribute:: isotensional

docs/source/physics/single_chain/swfjc/thermodynamics/isometric.rst

@@ -0,0 +1,15 @@
+SWFJC model thermodynamics (isometric)
+======================================
+
+.. toctree::
+   :maxdepth: 1
+
+   Legendre <isometric/legendre>
+
+.. autoclass:: polymers.physics.single_chain.swfjc.thermodynamics.isometric::SWFJC(number_of_links, link_length, hinge_mass, well_width)
+
+   .. autoattribute:: number_of_links
+   .. autoattribute:: link_length
+   .. autoattribute:: hinge_mass
+   .. autoattribute:: well_width
+   .. autoattribute:: legendre

docs/source/physics/single_chain/swfjc/thermodynamics/isometric/legendre.rst

@@ -0,0 +1,23 @@
+SWFJC model thermodynamics (isometric/legendre)
+===============================================
+
+.. autoclass:: polymers.physics.single_chain.swfjc.thermodynamics.isometric.legendre::SWFJC(number_of_links, link_length, hinge_mass, well_width)
+
+   .. autoattribute:: number_of_links
+   .. autoattribute:: link_length
+   .. autoattribute:: hinge_mass
+   .. autoattribute:: well_width
+   .. automethod:: force(end_to_end_length, temperature)
+   .. automethod:: nondimensional_force(nondimensional_end_to_end_length_per_link)
+   .. automethod:: helmholtz_free_energy(end_to_end_length, temperature)
+   .. automethod:: helmholtz_free_energy_per_link(end_to_end_length, temperature)
+   .. automethod:: relative_helmholtz_free_energy(end_to_end_length, temperature)
+   .. automethod:: relative_helmholtz_free_energy_per_link(end_to_end_length, temperature)
+   .. automethod:: nondimensional_helmholtz_free_energy(nondimensional_end_to_end_length_per_link, temperature)
+   .. automethod:: nondimensional_helmholtz_free_energy_per_link(nondimensional_end_to_end_length_per_link, temperature)
+   .. automethod:: nondimensional_relative_helmholtz_free_energy(nondimensional_end_to_end_length_per_link)
+   .. automethod:: nondimensional_relative_helmholtz_free_energy_per_link(nondimensional_end_to_end_length_per_link)
+   .. automethod:: equilibrium_distribution(end_to_end_length)
+   .. automethod:: nondimensional_equilibrium_distribution(nondimensional_end_to_end_length_per_link)
+   .. automethod:: equilibrium_radial_distribution(end_to_end_length)
+   .. automethod:: nondimensional_equilibrium_radial_distribution(nondimensional_end_to_end_length_per_link)

docs/src/physics/single_chain/efjc/thermodynamics.md

@@ -1,5 +1,6 @@
 # EFJC model thermodynamics
 
+  * [EFJC model thermodynamics (isometric)](../../../isometric)
   * [EFJC model thermodynamics (isotensional)](../../../isotensional)
 
 ```@autodocs

docs/src/physics/single_chain/efjc/thermodynamics/isometric.md

@@ -0,0 +1,8 @@
+# EFJC model thermodynamics (isometric)
+
+  * [EFJC model thermodynamics (isometric/asymptotic)](../../../../asymptotic)
+  * [EFJC model thermodynamics (isometric/legendre)](../../../../legendre)
+
+```@autodocs
+Modules = [Polymers.Physics.SingleChain.Efjc.Thermodynamics.Isometric]
+```

docs/src/physics/single_chain/efjc/thermodynamics/isometric/asymptotic.md

@@ -0,0 +1,9 @@
+# EFJC model thermodynamics (isometric/asymptotic)
+
+  * [EFJC model thermodynamics (isometric/asymptotic/alternative)](../../../../../alternative)
+  * [EFJC model thermodynamics (isometric/asymptotic/reduced)](../../../../../reduced)
+  * [EFJC model thermodynamics (isometric/asymptotic/legendre)](../../../../../legendre)
+
+```@autodocs
+Modules = [Polymers.Physics.SingleChain.Efjc.Thermodynamics.Isometric.Asymptotic]
+```

docs/src/physics/single_chain/efjc/thermodynamics/isometric/asymptotic/alternative.md

@@ -0,0 +1,7 @@
+# EFJC model thermodynamics (isometric/asymptotic/alternative)
+
+  * [EFJC model thermodynamics (isometric/asymptotic/alternative/legendre)](../../../../../../legendre)
+
+```@autodocs
+Modules = [Polymers.Physics.SingleChain.Efjc.Thermodynamics.Isometric.Asymptotic.Alternative]
+```

docs/src/physics/single_chain/efjc/thermodynamics/isometric/asymptotic/alternative/legendre.md

@@ -0,0 +1,5 @@
+# EFJC model thermodynamics (isometric/asymptotic/alternative/legendre)
+
+```@autodocs
+Modules = [Polymers.Physics.SingleChain.Efjc.Thermodynamics.Isometric.Asymptotic.Alternative.Legendre]
+```

docs/src/physics/single_chain/efjc/thermodynamics/isometric/asymptotic/legendre.md

@@ -0,0 +1,5 @@
+# EFJC model thermodynamics (isometric/asymptotic/legendre)
+
+```@autodocs
+Modules = [Polymers.Physics.SingleChain.Efjc.Thermodynamics.Isometric.Asymptotic.Legendre]
+```

docs/src/physics/single_chain/efjc/thermodynamics/isometric/asymptotic/reduced.md

@@ -0,0 +1,7 @@
+# EFJC model thermodynamics (isometric/asymptotic/reduced)
+
+  * [EFJC model thermodynamics (isometric/asymptotic/reduced/legendre)](../../../../../../legendre)
+
+```@autodocs
+Modules = [Polymers.Physics.SingleChain.Efjc.Thermodynamics.Isometric.Asymptotic.Reduced]
+```

docs/src/physics/single_chain/efjc/thermodynamics/isometric/asymptotic/reduced/legendre.md

@@ -0,0 +1,5 @@
+# EFJC model thermodynamics (isometric/asymptotic/reduced/legendre)
+
+```@autodocs
+Modules = [Polymers.Physics.SingleChain.Efjc.Thermodynamics.Isometric.Asymptotic.Reduced.Legendre]
+```

docs/src/physics/single_chain/efjc/thermodynamics/isometric/legendre.md

@@ -0,0 +1,5 @@
+# EFJC model thermodynamics (isometric/legendre)
+
+```@autodocs
+Modules = [Polymers.Physics.SingleChain.Efjc.Thermodynamics.Isometric.Legendre]
+```

docs/src/physics/single_chain/swfjc/thermodynamics.md

@@ -1,5 +1,6 @@
 # SWFJC model thermodynamics
 
+  * [SWFJC model thermodynamics (isometric)](../../../isometric)
   * [SWFJC model thermodynamics (isotensional)](../../../isotensional)
 
 ```@autodocs

docs/src/physics/single_chain/swfjc/thermodynamics/isometric.md

@@ -0,0 +1,7 @@
+# SWFJC model thermodynamics (isometric)
+
+  * [SWFJC model thermodynamics (isometric/legendre)](../../../../legendre)
+
+```@autodocs
+Modules = [Polymers.Physics.SingleChain.Swfjc.Thermodynamics.Isometric]
+```

docs/src/physics/single_chain/swfjc/thermodynamics/isometric/legendre.md

@@ -0,0 +1,5 @@
+# SWFJC model thermodynamics (isometric/legendre)
+
+```@autodocs
+Modules = [Polymers.Physics.SingleChain.Swfjc.Thermodynamics.Isometric.Legendre]
+```

src/physics/single_chain/efjc/thermodynamics/isometric/asymptotic/alternative/legendre/ex.rs

@@ -0,0 +1,50 @@
+#[no_mangle]
+pub extern fn physics_single_chain_efjc_thermodynamics_isometric_asymptotic_alternative_legendre_force(number_of_links: u8, link_length: f64, link_stiffness: f64, end_to_end_length: f64, temperature: f64) -> f64
+{
+    super::force(&number_of_links, &link_length, &link_stiffness, &end_to_end_length, &temperature)
+}
+#[no_mangle]
+pub extern fn physics_single_chain_efjc_thermodynamics_isometric_asymptotic_alternative_legendre_nondimensional_force(nondimensional_link_stiffness: f64, nondimensional_end_to_end_length_per_link: f64) -> f64
+{
+    super::nondimensional_force(&nondimensional_link_stiffness, &nondimensional_end_to_end_length_per_link)
+}
+#[no_mangle]
+pub extern fn physics_single_chain_efjc_thermodynamics_isometric_asymptotic_alternative_legendre_helmholtz_free_energy(number_of_links: u8, link_length: f64, hinge_mass: f64, link_stiffness: f64, end_to_end_length: f64, temperature: f64) -> f64
+{
+    super::helmholtz_free_energy(&number_of_links, &link_length, &hinge_mass, &link_stiffness, &end_to_end_length, &temperature)
+}
+#[no_mangle]
+pub extern fn physics_single_chain_efjc_thermodynamics_isometric_asymptotic_alternative_legendre_helmholtz_free_energy_per_link(number_of_links: u8, link_length: f64, hinge_mass: f64, link_stiffness: f64, end_to_end_length: f64, temperature: f64) -> f64
+{
+    super::helmholtz_free_energy_per_link(&number_of_links, &link_length, &hinge_mass, &link_stiffness, &end_to_end_length, &temperature)
+}
+#[no_mangle]
+pub extern fn physics_single_chain_efjc_thermodynamics_isometric_asymptotic_alternative_legendre_relative_helmholtz_free_energy(number_of_links: u8, link_length: f64, link_stiffness: f64, end_to_end_length: f64, temperature: f64) -> f64
+{
+    super::relative_helmholtz_free_energy(&number_of_links, &link_length, &link_stiffness, &end_to_end_length, &temperature)
+}
+#[no_mangle]
+pub extern fn physics_single_chain_efjc_thermodynamics_isometric_asymptotic_alternative_legendre_relative_helmholtz_free_energy_per_link(number_of_links: u8, link_length: f64, link_stiffness: f64, end_to_end_length: f64, temperature: f64) -> f64
+{
+    super::relative_helmholtz_free_energy_per_link(&number_of_links, &link_length, &link_stiffness, &end_to_end_length, &temperature)
+}
+#[no_mangle]
+pub extern fn physics_single_chain_efjc_thermodynamics_isometric_asymptotic_alternative_legendre_nondimensional_helmholtz_free_energy(number_of_links: u8, link_length: f64, hinge_mass: f64, nondimensional_link_stiffness: f64, nondimensional_end_to_end_length_per_link: f64, temperature: f64) -> f64
+{
+    super::nondimensional_helmholtz_free_energy(&number_of_links, &link_length, &hinge_mass, &nondimensional_link_stiffness, &nondimensional_end_to_end_length_per_link, &temperature)
+}
+#[no_mangle]
+pub extern fn physics_single_chain_efjc_thermodynamics_isometric_asymptotic_alternative_legendre_nondimensional_helmholtz_free_energy_per_link(number_of_links: u8, link_length: f64, hinge_mass: f64, nondimensional_link_stiffness: f64, nondimensional_end_to_end_length_per_link: f64, temperature: f64) -> f64
+{
+    super::nondimensional_helmholtz_free_energy_per_link(&number_of_links, &link_length, &hinge_mass, &nondimensional_link_stiffness, &nondimensional_end_to_end_length_per_link, &temperature)
+}
+#[no_mangle]
+pub extern fn physics_single_chain_efjc_thermodynamics_isometric_asymptotic_alternative_legendre_nondimensional_relative_helmholtz_free_energy(number_of_links: u8, nondimensional_link_stiffness: f64, nondimensional_end_to_end_length_per_link: f64) -> f64
+{
+    super::nondimensional_relative_helmholtz_free_energy(&number_of_links, &nondimensional_link_stiffness, &nondimensional_end_to_end_length_per_link)
+}
+#[no_mangle]
+pub extern fn physics_single_chain_efjc_thermodynamics_isometric_asymptotic_alternative_legendre_nondimensional_relative_helmholtz_free_energy_per_link(nondimensional_link_stiffness: f64, nondimensional_end_to_end_length_per_link: f64) -> f64
+{
+    super::nondimensional_relative_helmholtz_free_energy_per_link(&nondimensional_link_stiffness, &nondimensional_end_to_end_length_per_link)
+}